data_8GD1 # _model_server_result.job_id eRvja4sBQ8VOmDDdakLxWQ _model_server_result.datetime_utc '2024-12-27 03:11:23' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8gd1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":511}' # _entry.id 8GD1 # _exptl.entry_id 8GD1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 439.955 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,5S)-5-(aminomethyl)-N-(4-chloro-3-fluorophenyl)-1-[(3R,5S)-3,4,5-trimethylpiperazine-1-carbonyl]piperidine-3-carboxamide _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8GD1 _cell.length_a 59.965 _cell.length_b 65.218 _cell.length_c 87.283 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GD1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 13 A CYS 54 1_555 A SG CYS 33 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 78 A CYS 119 1_555 A SG CYS 91 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf3 A SG CYS 104 A CYS 218 1_555 A SG CYS 133 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 114 A CYS 228 1_555 A SG CYS 125 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 182 A CYS 296 1_555 A SG CYS 201 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 A SG CYS 247 A CYS 378 1_555 A SG CYS 308 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 A SG CYS 254 A CYS 385 1_555 A SG CYS 281 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 A SG CYS 264 A CYS 395 1_555 A SG CYS 273 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? covale ? covale1 A ND2 ASN 120 A ASN 234 1_555 B C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 127 A ASN 241 1_555 C C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 148 A ASN 262 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 162 A ASN 276 1_555 E C1 NAG . A NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale5 A ND2 ASN 175 A ASN 289 1_555 F C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 A ND2 ASN 181 A ASN 295 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 A ND2 ASN 255 A ASN 386 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 A ND2 ASN 261 A ASN 392 1_555 J C1 NAG . A NAG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale9 A ND2 ASN 311 A ASN 448 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale10 A ND2 ASN 324 A ASN 461 1_555 K C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? # _chem_comp.formula 'C21 H31 Cl F N5 O2' _chem_comp.formula_weight 439.955 _chem_comp.id Z1I _chem_comp.mon_nstd_flag . _chem_comp.name (3S,5S)-5-(aminomethyl)-N-(4-chloro-3-fluorophenyl)-1-[(3R,5S)-3,4,5-trimethylpiperazine-1-carbonyl]piperidine-3-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CL1 C18 Z1I sing 437 n n C20 C18 Z1I doub 438 n y C20 C21 Z1I sing 439 n y C18 C16 Z1I sing 440 n y C21 C14 Z1I doub 441 n y C16 F17 Z1I sing 442 n n C16 C15 Z1I doub 443 n y C14 C15 Z1I sing 444 n y C14 N13 Z1I sing 445 n n N13 C11 Z1I sing 446 n n C11 O12 Z1I doub 447 n n C11 C10 Z1I sing 448 n n C22 C10 Z1I sing 449 n n C22 C23 Z1I sing 450 n n C10 C09 Z1I sing 451 n n C23 C24 Z1I sing 452 n n C23 C26 Z1I sing 453 n n C24 N25 Z1I sing 454 n n C09 N08 Z1I sing 455 n n C26 N08 Z1I sing 456 n n N08 C07 Z1I sing 457 n n C28 N06 Z1I sing 458 n n C28 C29 Z1I sing 459 n n C07 N06 Z1I sing 460 n n C07 O27 Z1I doub 461 n n N06 C05 Z1I sing 462 n n C05 C03 Z1I sing 463 n n C30 C29 Z1I sing 464 n n C29 N02 Z1I sing 465 n n N02 C03 Z1I sing 466 n n N02 C01 Z1I sing 467 n n C03 C04 Z1I sing 468 n n C10 H1 Z1I sing 469 n n N13 H2 Z1I sing 470 n n C20 H3 Z1I sing 471 n n C21 H4 Z1I sing 472 n n C22 H5 Z1I sing 473 n n C22 H6 Z1I sing 474 n n C24 H7 Z1I sing 475 n n C24 H8 Z1I sing 476 n n C01 H9 Z1I sing 477 n n C01 H10 Z1I sing 478 n n C01 H11 Z1I sing 479 n n C03 H12 Z1I sing 480 n n C04 H13 Z1I sing 481 n n C04 H14 Z1I sing 482 n n C04 H15 Z1I sing 483 n n C05 H16 Z1I sing 484 n n C05 H17 Z1I sing 485 n n C09 H18 Z1I sing 486 n n C09 H19 Z1I sing 487 n n C15 H20 Z1I sing 488 n n C23 H21 Z1I sing 489 n n C26 H22 Z1I sing 490 n n C26 H23 Z1I sing 491 n n C28 H24 Z1I sing 492 n n C28 H25 Z1I sing 493 n n C29 H26 Z1I sing 494 n n C30 H27 Z1I sing 495 n n C30 H28 Z1I sing 496 n n C30 H29 Z1I sing 497 n n N25 H31 Z1I sing 498 n n N25 H32 Z1I sing 499 n n # _atom_sites.entry_id 8GD1 _atom_sites.fract_transf_matrix[1][1] 0.016676 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015333 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011457 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NAG A 1 501 502 NAG NAG . C 2 NAG A 1 502 503 NAG NAG . D 2 NAG A 1 503 504 NAG NAG . E 2 NAG A 1 504 505 NAG NAG . F 2 NAG A 1 505 506 NAG NAG . G 2 NAG A 1 506 507 NAG NAG . H 2 NAG A 1 507 509 NAG NAG . I 2 NAG A 1 508 511 NAG NAG . J 2 NAG A 1 509 512 NAG NAG . K 2 NAG A 1 510 513 NAG NAG . L 3 Z1I A 1 511 1 Z1I Z92 . M 4 EPE A 1 512 1 EPE EPE . N 5 CL A 1 513 1 CL CL . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C10 Z1I . . . L 3 -2.019 16.481 -12.693 1 55.01 ? C10 Z1I 511 A 1 HETATM 2 C C11 Z1I . . . L 3 -3.204 16.206 -13.662 1 57.54 ? C11 Z1I 511 A 1 HETATM 3 N N13 Z1I . . . L 3 -2.796 16.051 -15.08 1 51.55 ? N13 Z1I 511 A 1 HETATM 4 C C14 Z1I . . . L 3 -3.617 15.821 -16.297 1 40.64 ? C14 Z1I 511 A 1 HETATM 5 C C16 Z1I . . . L 3 -5.709 15.704 -17.471 1 52.44 ? C16 Z1I 511 A 1 HETATM 6 C C20 Z1I . . . L 3 -3.673 15.37 -18.665 1 58.55 ? C20 Z1I 511 A 1 HETATM 7 C C21 Z1I . . . L 3 -2.952 15.568 -17.49 1 47.03 ? C21 Z1I 511 A 1 HETATM 8 C C22 Z1I . . . L 3 -1.701 17.952 -12.737 1 48.1 ? C22 Z1I 511 A 1 HETATM 9 C C24 Z1I . . . L 3 -0.152 19.744 -12.002 1 67.73 ? C24 Z1I 511 A 1 HETATM 10 C C01 Z1I . . . L 3 -1.974 11.827 -6.908 1 85.49 ? C01 Z1I 511 A 1 HETATM 11 C C03 Z1I . . . L 3 -0.156 12.282 -7.964 1 73.6 ? C03 Z1I 511 A 1 HETATM 12 C C04 Z1I . . . L 3 0.576 10.975 -7.45 1 64.38 ? C04 Z1I 511 A 1 HETATM 13 C C05 Z1I . . . L 3 0.527 12.747 -9.298 1 71.46 ? C05 Z1I 511 A 1 HETATM 14 C C07 Z1I . . . L 3 0.025 15.137 -10.117 1 71.8 ? C07 Z1I 511 A 1 HETATM 15 C C09 Z1I . . . L 3 -2.18 16.095 -11.222 1 61.96 ? C09 Z1I 511 A 1 HETATM 16 C C15 Z1I . . . L 3 -4.995 15.904 -16.294 1 50.88 ? C15 Z1I 511 A 1 HETATM 17 C C18 Z1I . . . L 3 -5.05 15.437 -18.657 1 47.69 ? C18 Z1I 511 A 1 HETATM 18 C C23 Z1I . . . L 3 -0.324 18.237 -12.177 1 59.38 ? C23 Z1I 511 A 1 HETATM 19 C C26 Z1I . . . L 3 -0.148 17.554 -10.807 1 68.47 ? C26 Z1I 511 A 1 HETATM 20 C C28 Z1I . . . L 3 -1.688 13.169 -10.238 1 68.34 ? C28 Z1I 511 A 1 HETATM 21 C C29 Z1I . . . L 3 -2.223 12.9 -8.764 1 78.23 ? C29 Z1I 511 A 1 HETATM 22 C C30 Z1I . . . L 3 -3.665 12.328 -8.893 1 78.41 ? C30 Z1I 511 A 1 HETATM 23 F F17 Z1I . . . L 3 -7.07 15.772 -17.461 1 58.26 ? F17 Z1I 511 A 1 HETATM 24 N N02 Z1I . . . L 3 -1.468 12.008 -8.09 1 84.74 ? N02 Z1I 511 A 1 HETATM 25 N N06 Z1I . . . L 3 -0.376 13.716 -9.934 1 71.15 ? N06 Z1I 511 A 1 HETATM 26 N N08 Z1I . . . L 3 -0.799 16.241 -10.705 1 72.56 ? N08 Z1I 511 A 1 HETATM 27 N N25 Z1I . . . L 3 0.768 20.001 -10.901 1 68.47 ? N25 Z1I 511 A 1 HETATM 28 O O12 Z1I . . . L 3 -4.33 16.142 -13.288 1 52.24 ? O12 Z1I 511 A 1 HETATM 29 O O27 Z1I . . . L 3 1.12 15.411 -9.775 1 75.91 ? O27 Z1I 511 A 1 HETATM 30 CL CL1 Z1I . . . L 3 -5.951 15.177 -20.176 1 50.12 ? CL1 Z1I 511 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 30 #